Interleukin 7 Receptor Α Chain (IL7R) Shows Allelic and Functional
Total Page:16
File Type:pdf, Size:1020Kb
ARTICLES Interleukin 7 receptor a chain (IL7R) shows allelic and functional association with multiple sclerosis Simon G Gregory1,9, Silke Schmidt1,9, Puneet Seth2, Jorge R Oksenberg3, John Hart1, Angela Prokop1, Stacy J Caillier3, Maria Ban4, An Goris5, Lisa F Barcellos6, Robin Lincoln3, Jacob L McCauley7, Stephen J Sawcer4, D A S Compston4, Benedicte Dubois5, Stephen L Hauser3, Mariano A Garcia-Blanco2, Margaret A Pericak-Vance8 & Jonathan L Haines7, for the Multiple Sclerosis Genetics Group Multiple sclerosis is a demyelinating neurodegenerative disease with a strong genetic component. Previous genetic risk studies have failed to identify consistently linked regions or genes outside of the major histocompatibility complex on chromosome 6p. We describe allelic association of a polymorphism in the gene encoding the interleukin 7 receptor a chain (IL7R) as a significant risk factor for multiple sclerosis in four independent family-based or case-control data sets (overall P ¼ 2.9 Â 10–7). Further, the likely causal SNP, rs6897932, located within the alternatively spliced exon 6 of IL7R, has a functional effect on gene expression. http://www.nature.com/naturegenetics The SNP influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer. Multiple sclerosis is the prototypical human demyelinating disease, which requires multiple sources and types of positive evidence to and numerous epidemiological, adoption and twin studies have implicate a candidate gene, can be used to integrate both statistical provided evidence for a strong underlying genetic liability1.The and functional data. disease is most common in young adults, with more than 90% of Using genomic convergence3, we identified 28 genes that were affected individuals diagnosed before the age of 55, and fewer than 5% differentially expressed in at least two of nine previous expression diagnosed before the age of 14. Females are two to three times more studies (Supplementary Table 1 online). We focused on three genes frequently affected than males2, and the disease course can vary (interleukin 7 receptor alpha chain (IL7R) [MIM: 146661], matrix substantially, with some affected individuals suffering only minor metalloproteinase 19 (MMP19) [MIM: 601807] and chemokine (C-C disability several decades after their initial diagnosis, and others motif) ligand 2 (CCL2) [MIM: 158105]) that had a previously © Group 2007 Nature Publishing reaching wheelchair dependency shortly after disease onset. The published or inferred functional role in multiple sclerosis and that complex etiology of the disease and the currently undefined molecular were not located within the MHC. Two of the three genes localize to mechanisms of multiple sclerosis suggest that moderate contributions previous regions of genetic linkage on 17q12 (CCL2)4 and 5p13.2 from multiple risk loci underlie the development and progression of (IL7R)5. We analyzed a large data set of 760 US families of European the disease. descent, including 1,055 individuals with multiple sclerosis, and Many different approaches, including genetic linkage, candidate identified a significant association with multiple sclerosis susceptibility gene association and gene expression studies, have been used (sum- only for a nonsynonymous coding SNP (rs6897932) within a key marized in ref. 2) to identify the genetic basis of multiple sclerosis. transmembrane domain of IL7R. We subsequently replicated this However, genetic linkage screens have failed to identify consistent initial significant association in three independent European popula- regions of linkage outside of the major histocompatibility complex tions or populations of European descent: 438 individuals with (MHC). Candidate gene studies have suggested over 100 different multiple sclerosis and 479 unrelated controls ascertained in the United associated genes, but there has not been consensus acceptance of any States, 1,338 individuals with multiple sclerosis and their parents such candidates. Similarly, gene expression studies have identified ascertained in northern Europe (the UK and Belgium) and 1,077 hundreds of differentially expressed transcripts, with little consistency individuals with multiple sclerosis and 2,725 unrelated controls also across studies. The alternative approach of genomic convergence3, ascertained in northern Europe. We show that rs6897932 affects 1Center for Human Genetics, and 2Center for RNA Biology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA. 3Department of Neurology, University of California, San Francisco, California 94143, USA. 4Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK. 5Section for Experimental Neurology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium. 6School of Public Health, University of California, Berkeley, California 94720, USA. 7Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA. 8Miami Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida 33136, USA. 9These two authors contributed equally to this work. Correspondence should be addressed to J.L.H. ([email protected]) or M.A.P.-V. ([email protected]). Received 22 February; accepted 18 June; published online 29 July 2007; doi:10.1038/ng2103 NATURE GENETICS ADVANCE ONLINE PUBLICATION 1 ARTICLES Table 1 Clinical characteristics of the family-based and case-control multiple sclerosis data sets US data set European data set Affected individuals from Affected individuals from family-based data set Cases Controls family-based data set Cases Controls (n ¼ 1,055) (n ¼ 438) (n ¼ 479) (n ¼ 1,338) (n ¼ 1,077) (n ¼ 2,725) Mean age (and range), 41.6 (21–60) 44.6 (24–61) in years Mean age at onset 29.8 (3–63) 31.9 (11–60) 27.1 (9–53) 33.6 (10–62) (and range), in years Number of females 784 (74.3) 299 (68.3) 318 (66.4) 987 (74.0) 738 (68.5) 1350 (49.5) (and percentage) Disease type: n (%) Relapsing-remitting 552 (52.3) 365 (83.3) – – 1,152 (86.1) 875 (81.2) Secondary progressive 260 (24.6) 54 (12.3) – Progressive-relapsing 16 (1.5) 3 (0.7) – NA NA – Primary progressive 43 (4.1) 14 (3.2) – 80 (6.0) 146 (13.6) – Missing 184 (17.4) 2 (0.5) – 106 (7.9) 56 (5.2) – Mean disease duration 13.6 (0–50) 9.9 (0–44) – 10.8 (0–39) 16.4 (0–57) – (and range), in years Family-based US data set: 760 families (197 with multiple affected relatives (multiplex families), 563 with a single affected individual). Family-based European data set: 1,338 trios. UK affected individuals from trios: 64.8% relapsing-remitting, 27.4% secondary progressive. Unrelated UK affected individuals: 45.9% relapsing-remitting, 32.6% secondary progressive. For Belgian affected individuals, relapsing-remitting and secondary progressive multiple sclerosis were grouped together as ‘bout-onset’. http://www.nature.com/naturegenetics alternative splicing of exon 6, leading to increased skipping of the CCL2 and MMP19 (Supplementary Table 2 online), although this exon. This is predicted to increase production of soluble interleukin 7 does not exclude the possibility of a small effect of variants in either receptor alpha chain (IL7Ra) for individuals carrying the risk allele at gene. In the 760 US families (Table 1), the SNP having the strongest rs6897932. Our results strongly implicate the IL7Ra-related immune association with multiple sclerosis was rs6897932 (P ¼ 0.0006 by the response pathway in the etiology of multiple sclerosis. pedigree disequilibrium test (PDT)6), a nonsynonymous coding SNP (T244I) in exon 6 of IL7R, followed by rs11567705 (P ¼ 0.002) and RESULTS rs13188960 (P ¼ 0.002) (Table 2 and Fig. 1). The latter SNPs are in Initial analysis of CCL2, MMP19 and IL7R in US families strong linkage disequilibrium (LD) with rs6897932 (r2 ¼ 0.97 for None of the SNPs genotyped in IL7R, CCL2 or MMP19 strongly rs11567705, r2 ¼ 0.95 for rs13188960). The result for rs6897932 was deviated from Hardy-Weinberg equilibrium in a sample of unrelated due to overtransmission of the major allele (C) to offspring affected affected (P 4 0.04) or unaffected (P 4 0.10) individuals (P ¼ 0.05 for with multiple sclerosis. The risk allele frequency was similar in rs6897932 in affected individuals). We did not find any statistically individuals with multiple sclerosis who did or did not carry the significant evidence for association with multiple sclerosis for SNPs in multiple sclerosis–associated alleles HLA-DRB1*1501/1503 (0.79 and © Group 2007 Nature Publishing Table 2 PDT analysis of IL7R SNPs Minor/major Amino acid Overall PDT SNP Position (bp) allele MAF Gene region Type change P value rs13188960a 35889076 T/G 0.24 Upstream 0.0023 rs7718919 35891753 T/G 0.13 Upstream 0.8707 rs1389832a 35894478 T/C 0.34 Intron 1 0.0804 rs1494558a 35896825 A/G 0.34 Exon 2 Nonsynonymous I66T 0.0249 rs11567705 35896909 G/C 0.24 Intron 2 0.0018 rs969128 35896916 G/A 0.13 Intron 2 0.9343 rs1494555a 35906947 C/T 0.33 Exon 4 Nonsynonymous V138I 0.0327 rs7737000 35907030 T/C 0.13 Exon 4 Synonymous H165H 0.6801 rs1494554a 35909629 C/A 0.29 Intron 5 0.7175 rs6897932a 35910332 T/C 0.24 Exon 6 Nonsynonymous T244I 0.0006 rs987107a 35910984 T/C 0.29 Intron 6 0.7856 rs987106a 35911350 T/A 0.47 Intron 6 0.0134 rs3194051a 35912031 G/A 0.29 Exon 8 Nonsynonymous I356V 0.7856 rs1494571 35915844 C/G 0.28 Downstream 0.9276 P values meeting the Bonferroni-corrected significance threshold and respective